Interplay between chromatin and RNA processing

Inagaki, 2010, Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome, EMBO J, 29, 3496, 10.1038/emboj.2010.227 Miura, 2009, An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites, EMBO J, 28, 1078, 10.1038/emboj.2009.59 Saze, 2008, Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana, Science, 319, 462, 10.1126/science.1150987 Rigal, 2012, DNA methylation in an intron of the IBM1 histone demethylase gene stabilizes chromatin modification patterns, EMBO J, 31, 2981, 10.1038/emboj.2012.141 Mathieu, 2007, Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation, Cell, 130, 851, 10.1016/j.cell.2007.07.007 Lister, 2008, Highly integrated single-base resolution maps of the epigenome in Arabidopsis, Cell, 133, 523, 10.1016/j.cell.2008.03.029 Coustham, 2014, SHOOT GROWTH1 maintains Arabidopsis epigenomes by preventing ectopic DNA and histone methylation of gene bodies, PLoS ONE, 9, e84687, 10.1371/journal.pone.0084687 Saze, 2013, Mechanism for full-length RNA processing of Arabidopsis genes containing intragenic heterochromatin, Nat Commun, 4, 2301, 10.1038/ncomms3301 Wang, 2013, RNA-binding protein regulates plant DNA methylation by controlling mRNA processing at the intronic heterochromatin-containing gene IBM1, Proc Natl Acad Sci U S A, 110, 15467, 10.1073/pnas.1315399110 Sherstnev, 2012, Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation, Nat Struct Mol Biol, 19, 845, 10.1038/nsmb.2345 Ito, 2011, An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress, Nature, 472, 115, 10.1038/nature09861 Tsuchiya, 2013, Mutations in EDM2 selectively affect silencing states of transposons and induce plant developmental plasticity, Sci Rep, 3, 1701, 10.1038/srep01701 Eulgem, 2007, EDM2 is required for RPP7-dependent disease resistance in Arabidopsis and affects RPP7 transcript levels, Plant J, 49, 829, 10.1111/j.1365-313X.2006.02999.x Tsuchiya, 2013, An alternative polyadenylation mechanism coopted to the Arabidopsis RPP7 gene through intronic retrotransposon domestication, Proc Natl Acad Sci U S A, 110, E3535, 10.1073/pnas.1312545110 Lei, 2014, Arabidopsis EDM2 promotes IBM1 distal polyadenylation and regulates genome DNA methylation patterns, Proc Natl Acad Sci U S A, 111, 527, 10.1073/pnas.1320106110 Cowley, 2012, Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus, Nucleic Acids Res, 40, 8917, 10.1093/nar/gks654 Wood, 2008, Regulation of alternative polyadenylation by genomic imprinting, Genes Dev, 22, 1141, 10.1101/gad.473408 Sonmez, 2011, RNA 3′ processing functions of Arabidopsis FCA and FPA limit intergenic transcription, Proc Natl Acad Sci U S A, 108, 8508, 10.1073/pnas.1105334108 Liu, 2010, Targeted 3′ processing of antisense transcripts triggers Arabidopsis FLC chromatin silencing, Science, 327, 94, 10.1126/science.1180278 Hornyik, 2010, The spen family protein FPA controls alternative cleavage and polyadenylation of RNA, Dev Cell, 18, 203, 10.1016/j.devcel.2009.12.009 Ietswaart, 2012, Flowering time control: another window to the connection between antisense RNA and chromatin, Trends Genet, 28, 445, 10.1016/j.tig.2012.06.002 Baurle, 2007, Widespread role for the flowering-time regulators FCA and FPA in RNA-mediated chromatin silencing, Science, 318, 109, 10.1126/science.1146565 Law, 2010, Establishing, maintaining and modifying DNA methylation patterns in plants and animals, Nat Rev Genet, 11, 204, 10.1038/nrg2719 Zemach, 2013, The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin, Cell, 153, 193, 10.1016/j.cell.2013.02.033 Zhang, 2011, RNA-directed DNA methylation, Curr Opin Plant Biol, 14, 142, 10.1016/j.pbi.2011.02.003 Matzke, 2009, RNA-mediated chromatin-based silencing in plants, Curr Opin Cell Biol, 21, 367, 10.1016/j.ceb.2009.01.025 Haag, 2012, In vitro transcription activities of Pol IV, Pol V, and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing, Mol Cell, 48, 811, 10.1016/j.molcel.2012.09.027 Wierzbicki, 2009, RNA polymerase V transcription guides ARGONAUTE4 to chromatin, Nat Genet, 41, 630, 10.1038/ng.365 Zheng, 2009, Intergenic transcription by RNA polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis, Genes Dev, 23, 2850, 10.1101/gad.1868009 Li, 2006, An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana, Cell, 126, 93, 10.1016/j.cell.2006.05.032 Wahl, 2009, The spliceosome: design principles of a dynamic RNP machine, Cell, 136, 701, 10.1016/j.cell.2009.02.009 Morris, 2008, The Cajal body, Biochim Biophys Acta, 1783, 2108, 10.1016/j.bbamcr.2008.07.016 Pontes, 2006, The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center, Cell, 126, 79, 10.1016/j.cell.2006.05.031 Cao, 2002, Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing, Curr Biol, 12, 1138, 10.1016/S0960-9822(02)00925-9 Ausin, 2012, The splicing factor SR45 affects the RNA-directed DNA methylation pathway in Arabidopsis, Epigenetics, 7, 29, 10.4161/epi.7.1.18782 Ali, 2007, Regulation of plant developmental processes by a novel splicing factor, PLoS ONE, 2, e471, 10.1371/journal.pone.0000471 Zhang, 2013, The splicing machinery promotes RNA-directed DNA methylation and transcriptional silencing in Arabidopsis, EMBO J, 32, 1128, 10.1038/emboj.2013.49 Dou, 2013, The PRP6-like splicing factor STA1 is involved in RNA-directed DNA methylation by facilitating the production of Pol V-dependent scaffold RNAs, Nucleic Acids Res, 41, 8489, 10.1093/nar/gkt639 Lee, 2006, STABILIZED1, a stress-upregulated nuclear protein, is required for pre-mRNA splicing, mRNA turnover, and stress tolerance in Arabidopsis, Plant Cell, 18, 1736, 10.1105/tpc.106.042184 Huang, 2013, A pre-mRNA-splicing factor is required for RNA-directed DNA methylation in Arabidopsis, PLoS Genet, 9, e1003779, 10.1371/journal.pgen.1003779 Xiong, 2013, Core small nuclear ribonucleoprotein particle splicing factor SmD1 modulates RNA interference in Drosophila, Proc Natl Acad Sci U S A, 110, 16520, 10.1073/pnas.1315803110 Bayne, 2008, Splicing factors facilitate RNAi-directed silencing in fission yeast, Science, 322, 602, 10.1126/science.1164029 Tabach, 2013, Identification of small RNA pathway genes using patterns of phylogenetic conservation and divergence, Nature, 493, 694, 10.1038/nature11779 Elkon, 2013, Alternative cleavage and polyadenylation: extent, regulation and function, Nat Rev Genet, 14, 496, 10.1038/nrg3482